I set up a small consulting company in 2010 and it is an LLC and I got permission for an S corp. I work as a consultant and have received checks in the corporate name but also checks in my name. My question is can I count the 1099 income as company income? Since many people know me I got checks made out to me instead of the company. How do I report the 1099 income?

If you do not report 1099 received in your name on your tax return, you will get letter from IRS. So you must report as your income on schedule C. Also on this schedule report payments made to LLC.